Simultaneous comparisons of diversity indices estimated from metagenomic data

The following “GlobalPatterns” data set is from the phyloseq package on Bioconductor. This packages allows the import of OTU-tables from qiime, mothur and other software packages for sequence data. Once the data is imported into R, it is stored in a phyloseq object, which is a specialized system of S4-classes.

First, we install phyloseq with dependencies from Bioconductor if not already installed.

> source("http://bioconductor.org/biocLite.R")
> biocLite("phyloseq")

Next, we load the phyloseq packages to get the GlobalPatterns data set. For pre-processing steps of the sequence data, see the phyloseq vignettes.

> library(phyloseq)
> data(GlobalPatterns)
> GP <- prune_species(speciesSums(GlobalPatterns) > 0, GlobalPatterns)

Phyloseq offers several functions to access variables in the object.

> sample_variables(GlobalPatterns)

## [1] "X.SampleID"               "Primer"                  
## [3] "Final_Barcode"            "Barcode_truncated_plus_T"
## [5] "Barcode_full_length"      "SampleType"              
## [7] "Description"

> plot_richness(GP, x = "SampleType", color = "SampleType", shsi = TRUE)

Will be continued soon…